WSNetChop_3_1

By | September 22, 2011

INTRODUCTION

This Web Service implements NetChop v. 3.1. It produces neural network
predictions for cleavage sites of the human proteasome. The method is
described in detail in the following article:

The role of the proteasome in generating cytotoxic T cell epitopes:
Insights obtained from improved predictions of proteasomal cleavage.
M Nielsen, C Lundegaard, O Lund, and C Kesmir.
Immunogenetics., 57(1-2):33-41, 2005.

Alongside this Web Service the NetChop method is also implemented as
a traditional click-and-paste WWW server at:

http://www.cbs.dtu.dk/services/NetChop/

NetChop is also available as a stand-alone software package to install
and run at the user’s site, with the same functionality. For academic
users there is a download page at:

http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netchop

Other users are requested to write to software@cbs.dtu.dk for details.

WEB SERVICE OPERATION

This Web Service is fully asynchronous; the usage is split into the
following three operations:

1. runService

Input: The following parameters and data:

* ‘method’ – prediction method
0 for “C term 3.0″, 1 for “20S 3.0″;

* ‘threshold’ – threshold for yes/no decision
The default is 0.5; increasing the threshold results in better
specificity, but worse sensitivity

* ‘sequences’ – protein sequences, with unique identifiers
The sequences must be written using the one letter amino acid code:
`acdefghiklmnpqrstvwy’ or `ACDEFGHIKLMNPQRSTVWY’. Other letters
will be converted to `X’ and treated as unknown amino acids.
Other symbols, such as whitespace and numbers, will be ignored.

Output: Unique job identifier

2. pollQueue

Input: Unique job identifier

Output: ‘jobstatus’ – the status of the job
Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED,
UNKNOWN JOBID or QUEUE DOWN

3. fetchResult

Input: Unique job identifier of a finished job

Output: ‘output’ – prediction results
For each input residue a record is output consisting of the
following fields:

seqname truncated to 10 characters in ver. 3.1a
source “netchop-3.1a” (fixed string)
feature “cleavage” (fixed string)
start,end residue number (given twice)
score prediction score
strand,frame N/A
comment answer (“S” for yes, “.” for no)

CONTACT

Questions concerning the scientific aspects of the NetChop method should go
to Morten Nielsen, mniel@cbs.dtu.dk; technical question concerning the Web
Service should go to Peter Fischer Hallin, pfh@cbs.dtu.dk or Kristoffer
Rapacki, rapacki@cbs.dtu.dk.

Name
WSNetChop_3_1
Documentation
http://www.cbs.dtu.dk/services/NetChop/
http://www.cbs.dtu.dk/ws/ws.php?entry=NetChop
Protocol
SOAP
WSDL
Endpoint
http://ws.cbs.dtu.dk/cgi-bin/soap/ws/server.cgi
Topic
Biology
Type
Tags
, , ,
Description

INTRODUCTION This Web Service implements NetChop v. 3.1. It produces neural network predictions for cleavage sites of the human proteasome. [...]

Further information

INTRODUCTION

This Web Service implements NetChop v. 3.1. It produces neural network
predictions for cleavage sites of the human proteasome. The method is
described in detail in the following article:

The role of the proteasome in generating cytotoxic T cell epitopes:
Insights obtained from improved predictions of proteasomal cleavage.
M Nielsen, C Lundegaard, O Lund, and C Kesmir.
Immunogenetics., 57(1-2):33-41, 2005.

Alongside this Web Service the NetChop method is also implemented as
a traditional click-and-paste WWW server at:

http://www.cbs.dtu.dk/services/NetChop/

NetChop is also available as a stand-alone software package to install
and run at the user’s site, with the same functionality. For academic
users there is a download page at:

http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netchop

Other users are requested to write to software@cbs.dtu.dk for details.

WEB SERVICE OPERATION

This Web Service is fully asynchronous; the usage is split into the
following three operations:

1. runService

Input: The following parameters and data:

* ‘method’ – prediction method
0 for “C term 3.0″, 1 for “20S 3.0″;

* ‘threshold’ – threshold for yes/no decision
The default is 0.5; increasing the threshold results in better
specificity, but worse sensitivity

* ‘sequences’ – protein sequences, with unique identifiers
The sequences must be written using the one letter amino acid code:
`acdefghiklmnpqrstvwy’ or `ACDEFGHIKLMNPQRSTVWY’. Other letters
will be converted to `X’ and treated as unknown amino acids.
Other symbols, such as whitespace and numbers, will be ignored.

Output: Unique job identifier

2. pollQueue

Input: Unique job identifier

Output: ‘jobstatus’ – the status of the job
Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED,
UNKNOWN JOBID or QUEUE DOWN

3. fetchResult

Input: Unique job identifier of a finished job

Output: ‘output’ – prediction results
For each input residue a record is output consisting of the
following fields:

seqname truncated to 10 characters in ver. 3.1a
source “netchop-3.1a” (fixed string)
feature “cleavage” (fixed string)
start,end residue number (given twice)
score prediction score
strand,frame N/A
comment answer (“S” for yes, “.” for no)

CONTACT

Questions concerning the scientific aspects of the NetChop method should go
to Morten Nielsen, mniel@cbs.dtu.dk; technical question concerning the Web
Service should go to Peter Fischer Hallin, pfh@cbs.dtu.dk or Kristoffer
Rapacki, rapacki@cbs.dtu.dk.

Original source
BioCatalogue

Leave Your Comment

Your email will not be published or shared. Required fields are marked *

*

*

You may use these HTML tags and attributes: <a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <strike> <strong>